In a manager career which began before his 30th birthday, he was in charge of several club and national teams, including Athletic Bilbao which he also represented as a player, Espanyol and Spain. He won the La Liga championship in 1983 and 1984 with the latter.

Clemente's best La Liga output with his first and only club consisted of 18 games in the 1969–70 campaign. On 23 November 1969, during a league match against CE Sabadell FC, he suffered a serious leg injury (fibula and tibia) from which he never fully recovered; after four unsuccessful operations, he retired aged just 24.

In the 1981 summer, 31-year-old Clemente was appointed at Athletic Bilbao. He led the side to back-to-back national championships in his second[5] and third years but, during this timeframe, also began a bitter rivalry with César Luis Menotti and his FC Barcelona – the Argentine criticized his playing style as authoritarian and his teams as defensive and destructive, and the Spaniard in turn dismissed Menotti as an ageing hippy and womanizer; the culmination of this was the 1984 final of the Copa del Rey, which ended in a massive brawl between the two sets of players.

In 1992 Clemente was appointed manager of Spain, replacing Vicente Miera after the nation had failed to qualify for UEFA Euro 1992. His first game in charge was a 1–0 friendly win over England on 9 September, and he led the country to the following three major international tournaments, the 1994 and 1998FIFA World Cups and Euro 1996, being eliminated in the group stage of the second competition[8] and having a run of 31 matches without defeat.

Clemente became manager of the Serbian national team on 21 July 2006, being brought in on initiative from Serbian Football Association president Zvezdan Terzić. According to local media his salary was €30,000 per month on a two-year contract, worth €720,000 in total – also, he was eligible for a €400,000 bonus if the country qualified for Euro 2008, and an additional €150,000 bonus for every round passed at the tournament; in an interview given to Serbian daily Politika, he claimed his current was the lowest wage he had earned in the last 20 years.[13]

On 13 February 2012 Clemente signed as the new manager of Sporting de Gijón, with a contract running until the end of the season.[21] He left the Asturians in May, following their relegation;[22] in the process he celebrated his 500th game in the Spanish first division, a 1–2 away loss to Granada CF.[23]